I think those remarks about space/nature being the enemy were simply intended as a misdirection aimed at the fans, courtesy of JJ's obsession with secrecy and surprise. Not unlike when Karl Urban "accidentally" let it slip that Cumberbatch was playing Gary Mitchell in STID. Just another red herring.
War with the Klingons. Tragic romance with Carol Marcus (in the end she takes the kid and leaves). Maybe the return of Khan and/or repercussions from Kirk's blood transfusion from Khan. That's my call.